The long term effects of the arrival of the Spanish on the population of South America were simply catastrophic. While this is the case for every group of Native-Americans that encountered Europeans from the fifteenth century onwards, the Incan population suffered a dramatic and quick decline following contact. It is estimated that parts of the empire, notably the Central Andes, suffered a population decline ratio of 58:1 during the years of 1520-1571.
The single greatest cause of the demise of native populations was disease. Old World diseases brought over unknowingly by colonists and conquistadors wreaked havoc on native populations at a greater rate than any army or armed conflict. The fact that the Inca did not have as strong of a writing tradition as the Aztecs or Maya is one reason why it is more difficult to estimate population decline or any events after subjugation. However, it is apparent that illness from the Spaniards predated their actual presence in the region by several years. The outbreak, believed to be hemorrhagic smallpox, entered the Andes in 1524. While numbers are unavailable, Spanish records indicate that the population was so devastated by disease that their forces could hardly be resisted. However, whether the illness of the 1520s was actually smallpox has been contested; a minority of scholars claim that the epidemic was actually due to an indigenous illness called Carrion's disease. In any case, a study by N. D. Cook, the results of which were published in 1981, show that the Andes suffered from three separate population declines during colonization. The first was of 30-50 percent during the first outbreak of smallpox. Then, when smallpox was followed with the measles, another decline of 25-30 percent occurred. Finally, when smallpox and measles appeared together, which occurred from 1585 to 1591, a decline of 30-60 percent occurred. Collectively these declines amounted to a decline of 93 percent from the population pre-contact in the Andes region.
Beyond the devastation of the local populations by disease, there was also considerable enslavement, pillaging and destruction from warfare. Thousands of women were taken from the local populations by the Spanish and used by conquistadors as personal vassals. As Pizarro and his men took over portions of South America they plundered and enslaved countless people. There are some Spanish documents that suggest that the local populations entered into vassalage willingly, but these are likely cases of people being threatened with death after the destruction of their region. The basic policy of the Spanish towards local populations was that voluntary vassalage would yield safety and coexistence while continued resistance would lead to more death and destruction.
Another significant effect on the people in South America was the spread of Christianity. As Pizarro and the Spanish subdued the continent and brought it under their control, they forcefully converted many to Christianity, claiming to have educated them in the ways of the "one true religion." With the destruction of the local populations along with the capitulation of the Inca Empire, the Spanish missionary work after colonization began was able to continue unimpeded. It took just a generation for the entire continent to be under Christian influence.